Ian Hunter told the Royal Commission on Thursday he felt Mr Hayes was attempting to pour water over child sex allegations levelled at Gerard Vincent Byrnes after they first surfaced in September 2007.

Barrister Patrick Quinn, who represents Christopher Fry, asked Mr Hunter whether he came to that conclusion as a result of information he received from Mr Hayes shortly after the meeting with child victim KH, her father and the school's student protection officer Catherine Long.

"In hindsight, from other information that I have received since, yes, it would certainly appear to me that was happening," Mr Hunter said.

"That is correct, and the specific point of my questioning and looking for detail in each of those cases was to make sure that there was not any sexual abuse taking place."

Barrister Jane Needham, representing the Toowoomba Diocese, then claimed Mr Hunter and Mr Fry had colluded in the evidence they had given the commission.

"Did you and he discuss matters before making your statements?" she asked.

"No," Mr Hunter replied.

"Did you and Mr Fry consult the contents of your statements to the royal commission?" she asked.

"No," he replied.

Mr Fry then admitted under a barrage of questions from Ms Needham he failed to follow up the allegations levelled at Byrnes.

"I certainly wish I had done that," he said.

"It was at the end of the term when I was preparing that report.

"We would have finished off all the other work from the term first before going off on annual leave."

The commission was then told of another sexual allegation Mr Hunter investigated for the Catholic Education Office at another school in Toowoomba the previous year.

The Royal Commission is expected to hear evidence today (Feb 21) from former Toowoomba Bishop William Morris.